## [1] "O76_p2_con_R1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
79,798,526 |
79,798,526 |
| Not Truncated |
47,325,884 |
45,444,772 |
| Truncated |
32,472,642 |
34,353,754 |
Truncated Read Length
| Average Length Truncated |
46.7 |
45.5 |
Mapping Efficiency
| Too Short To Map |
5,055,767 |
6,668,530 |
| Unique Alignments |
68,792,703 |
65,684,615 |
| Multiple Alignments |
2,830,524 |
2,814,942 |
| Failed To Align |
3,119,532 |
4,630,439 |
| Paired |
57,256,244 |
57,256,244 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
28,644,437 |
| Invalid Pairs |
28,611,807 |
| Same Circularised |
39,369 |
| Same Dangling Ends |
2,882,646 |
| Same Fragment Internal |
12,270,527 |
| Re Ligation |
11,367,397 |
| Contiguous Sequence |
301,278 |
| Wrong Size |
1,750,590 |
| Total Pairs |
57,256,244 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
28,644,437 |
41,137 |
| Cis-close (<10Kbp) |
2,604,284 |
3,862 |
| Cis-far (>10Kbp) |
19,851,079 |
22,948 |
| Trans |
6,189,074 |
14,327 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
